How do I determine NodeTree overhead in a .blend file?
This should not affect anything significantly. I have already added a few of my own nodegroups and a couple node groups from the b&deg;wide nodepack to my startup.blend and have noticed no side effects.

Nodegroups don't really affect performance (unless they are being used), the biggest thing would be file size (which you probably don't have to worry about, because they don't take up much space).